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- PDB-1yfo: RECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA, DOMAIN 1 FROM MOUSE -

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Basic information

Entry
Database: PDB / ID: 1yfo
TitleRECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA, DOMAIN 1 FROM MOUSE
ComponentsRECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA
KeywordsHYDROLASE / SIGNAL TRANSDUCTION / RECEPTOR / GLYCOPROTEIN / PHOSPHORYLATION
Function / homology
Function and homology information


NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / regulation of focal adhesion assembly / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / integrin-mediated signaling pathway / synaptic membrane ...NCAM signaling for neurite out-growth / RAF/MAP kinase cascade / regulation of focal adhesion assembly / protein tyrosine phosphatase activity / protein-tyrosine-phosphatase / protein tyrosine phosphatase activity, metal-dependent / histone H2AXY142 phosphatase activity / non-membrane spanning protein tyrosine phosphatase activity / integrin-mediated signaling pathway / synaptic membrane / modulation of chemical synaptic transmission / Schaffer collateral - CA1 synapse / insulin receptor signaling pathway / receptor complex / focal adhesion / membrane
Similarity search - Function
Receptor tyrosine-protein phosphatase alpha / Receptor tyrosine-protein phosphatase, alpha/epsilon-type / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic ...Receptor tyrosine-protein phosphatase alpha / Receptor tyrosine-protein phosphatase, alpha/epsilon-type / : / Protein tyrosine phosphatase superfamily / Protein-Tyrosine Phosphatase; Chain A / Protein tyrosine phosphatase, catalytic domain / PTP type protein phosphatase domain profile. / Protein-tyrosine phosphatase / Tyrosine-specific protein phosphatase, PTPase domain / Protein-tyrosine phosphatase, catalytic / Protein tyrosine phosphatase, catalytic domain motif / Tyrosine specific protein phosphatases active site. / Protein-tyrosine phosphatase, active site / Tyrosine-specific protein phosphatases domain / Tyrosine specific protein phosphatases domain profile. / Protein-tyrosine phosphatase-like / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Receptor-type tyrosine-protein phosphatase alpha
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsBilwes, A.M. / Noel, J.P.
CitationJournal: Nature / Year: 1996
Title: Structural basis for inhibition of receptor protein-tyrosine phosphatase-alpha by dimerization.
Authors: Bilwes, A.M. / den Hertog, J. / Hunter, T. / Noel, J.P.
History
DepositionDec 11, 1996Processing site: BNL
Revision 1.0Apr 1, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_ref_seq_dif.details
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA
B: RECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA


Theoretical massNumber of molelcules
Total (without water)69,7902
Polymers69,7902
Non-polymers00
Water5,170287
1
A: RECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA


Theoretical massNumber of molelcules
Total (without water)34,8951
Polymers34,8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA


Theoretical massNumber of molelcules
Total (without water)34,8951
Polymers34,8951
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.190, 119.840, 61.180
Angle α, β, γ (deg.)90.00, 110.08, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.999983, 0.001238, -0.005715), (0.001228, -0.999998, -0.001822), (-0.005717, 0.001814, -0.999982)
Vector: 0.134, -31.4184, 58.1333)

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Components

#1: Protein RECEPTOR PROTEIN TYROSINE PHOSPHATASE ALPHA / D1


Mass: 34894.770 Da / Num. of mol.: 2 / Fragment: MEMBRANE PROXIMAL CATALYTIC DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: TYPE I MEMBRANE PROTEIN / Cell line: BL21 / Cell line (production host): BL21 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): 293 / References: UniProt: P18052, protein-tyrosine-phosphatase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Compound detailsRESIDUES 379 - 386 WERE NOT MODELLED FOR EACH MONOMER TRYPSIN CUT AT 385 OR 386.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.08 Å3/Da / Density % sol: 44 %
Crystal growpH: 5
Details: PROTEIN WAS CRYSTALLIZED FROM 12% PEG 8000 0.3 M AMMONIUM ACETATE, 50 MM SODIUM ACETATE PH 5, 2 MM DTT. ETHYLENE GLYCOL 20% WAS USED AS A CRYOPROTECTANT., pH 5.0
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
115-20 mg/mlprotein1drop
250 mMsodium acetate1reservoir
30.3 Mammonium acetate1reservoir
412 %(w/v)PEG80001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE M18X / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: Jul 14, 1995 / Details: MIRRORS
RadiationMonochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→23 Å / Num. obs: 22317 / % possible obs: 82.4 % / Observed criterion σ(I): 0 / Redundancy: 2.6 % / Biso Wilson estimate: 27 Å2 / Rsym value: 0.046 / Net I/σ(I): 22
Reflection shellResolution: 2.25→2.35 Å / Redundancy: 1 % / Mean I/σ(I) obs: 7 / Rsym value: 0.104 / % possible all: 17.4
Reflection
*PLUS
Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 17.4 % / Rmerge(I) obs: 0.104

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2HNP

2hnp


Resolution: 2.25→20 Å / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.251 -8.1 %RANDOM
Rwork0.184 ---
obs0.184 22277 82.4 %-
Refinement stepCycle: LAST / Resolution: 2.25→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4562 0 0 287 4849
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.007
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d24.16
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.19
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
LS refinement shellResolution: 2.25→2.35 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.324 -1.8 %
Rwork0.281 533 -
obs--17.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARHCSDX.PROTOPHCSDX.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg24.16
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.19
LS refinement shell
*PLUS
Rfactor obs: 0.281

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